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Biological Magnetic Resonance Data Bank


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BMRB Entry 34146

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34146
MolProbity Validation Chart

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Title: Solution Structure of the N-terminal Region of Dkk4   PubMed: 29925589

Deposition date: 2017-06-01 Original release date: 2018-06-07

Authors: Waters, L.; Patel, S.; Barkell, A.; Muskett, F.; Robinson, M.; Holdsworth, G.; Carr, M.

Citation: Patel, S.; Barkell, A.; Gupta, D; Strong, S.; Bruton, S.; Muskett, F.; Addis, P.; Renshaw, P.; Slocombe, P.; Doyle, C.; Cargo, A.; Taylor, R.; Prosser, C.; Henry, A.; Robinson, M.; Waters, L.; Holdsworth, G.; Carr, M.. "Structural and functional analysis of Dickkopf 4 (Dkk4): New insights into Dkk evolution and regulation of Wnt signaling by Dkk and Kremen proteins"  J. Biol. Chem. 293, 12149-12166 (2018).

Assembly members:
Dickkopf-related protein 4, polymer, 95 residues, 10931.425 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
Dickkopf-related protein 4: MLVLDFNNIRSSADLHGARK GSQCLSDTDCNTRKFCLQPR DEKPFCATCRGLRRRCQRDA MCCPGTLCVNDVCTTMEDAT ENLYFQSLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts308
15N chemical shifts76
1H chemical shifts528

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 95 residues - 10931.425 Da.

1   METLEUVALLEUASPPHEASNASNILEARG
2   SERSERALAASPLEUHISGLYALAARGLYS
3   GLYSERGLNCYSLEUSERASPTHRASPCYS
4   ASNTHRARGLYSPHECYSLEUGLNPROARG
5   ASPGLULYSPROPHECYSALATHRCYSARG
6   GLYLEUARGARGARGCYSGLNARGASPALA
7   METCYSCYSPROGLYTHRLEUCYSVALASN
8   ASPVALCYSTHRTHRMETGLUASPALATHR
9   GLUASNLEUTYRPHEGLNSERLEUGLUHIS
10   HISHISHISHISHIS

Samples:

sample_1: Dkk4n, [U-13C; U-15N], 140 uM; Sodium Phosphate 25 mM; NaCl 100 mM; Sodium Azide .02%

sample_2: Dkk4n, [U-15N], 210 uM; Sodium Phosphate 25 mM; NaCl 100 mM; Sodium Azide .02%

sample_3: Dkk4n, [U-15N], 90 uM; Sodium Phosphate 25 mM; NaCl 100 mM; Sodium Azide .02%

sample_4: Dkk4n, [U-13C; U-15N], 140 uM; Sodium Phosphate 25 mM; NaCl 100 mM; Sodium Azide .02%

sample_5: Dkk4n, [U-13C; U-15N], 230 uM; Sodium Phosphate 25 mM; NaCl 100 mM; Sodium Azide .02%

sample_conditions_1: ionic strength: 150 mM; pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
3D TROSY-HNCACBsample_1isotropicsample_conditions_1
3D TROSY-HN(CO)CACBsample_1isotropicsample_conditions_1
3D TROSY-HNCOsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
2D TROSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1
3D 13C/1H HSQC-NOESYsample_5isotropicsample_conditions_1
3D 13C/1H HSQC-NOESYsample_5isotropicsample_conditions_1
3D 15N/1H NOESY-HSQCsample_2isotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY vNMRFAM-Sparky 1.4, Goddard - data analysis

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AVIII 600 MHz
  • Bruker AVII 800 MHz
  • Bruker AvanceIII HD 950 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts